From e4f218f8d1f6ed165ddeb18661b010e4f99af578 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 14 Jun 2012 14:52:35 +0200
Subject: [PATCH] Extended documentation of AddChain() according to BZDNG-285.
---
modules/mol/base/doc/entity.rst | 33 ++++++++++++++++++++++++---------
1 file changed, 24 insertions(+), 9 deletions(-)
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 94b8a1b3b..5418b813a 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -856,19 +856,35 @@ The View Classes
Returns a copy of this entity. Provided for `duck-typing <http://en.wikipedia.org/wiki/Duck_typing>` purposes.
- :rtype: EntityView
-
+ :rtype: :class:`EntityView`
+
.. method:: AddChain(chain_handle[, view_add_flags])
Add chain to view. By default, only the chain is added to the view, but not
- its residues and atoms. This behavior can be changed by passing in an
- appropriate set of `view_add_flags`
-
+ its residues and atoms. This behaviour can be changed by passing in an
+ appropriate set of `view_add_flags`.
+
+ The following example just adds a chain without residues and atoms:
+
+ .. code-block:: python
+
+ pdb = ost.io.LoadPDB(<PDB file name>)
+ v = pdb.CreateEmptyView()
+ v.AddChain(pdb.chains[0])
+
+ To **copy** a whole chain, go like:
+
+ .. code-block:: python
+
+ pdb = ost.io.LoadPDB(<PDB file name>)
+ v = pdb.CreateEmptyView()
+ v.AddChain(pdb.chains[0], ost.mol.INCLUDE_ALL)
+
:param chain_handle:
:type chain_handle: ChainHandle
:param view_add_flags: An ORed together combination of `view_add_flags`.
- :type view_add_flags: int
- :rtype: class:`ChainView`
+ :type view_add_flags: :class:`int`
+ :rtype: :class:`ChainView`
.. method:: AddResidue(residue_handle[, view_add_flags])
@@ -881,7 +897,7 @@ The View Classes
:type residue_handle: ResidueHandle
:param view_add_flags:
:type view_add_flags: int
- :rtype: class:`ResidueView`
+ :rtype: :class:`ResidueView`
.. method:: AddAtom(atom_handle[, view_add_flags])
@@ -1617,4 +1633,3 @@ ChainType functions
:raises: :class:`runtime_error` if **type** is unrecognised.
:returns: :class:`str`
-
--
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